Abstract
Structure-based virtual screening is a technology increasingly used in drug discovery. Although successful at estimating binding modes for input ligands, these technologies are less successful at ranking true hits correctly by binding free energy. This paper presents the results of initial attempts to automate the removal of false positives from virtual hit sets, by evolving a post docking filter using Cartesian Genetic Programming.
Keywords
- Virtual Screening
- Native Ligand
- Cartesian Genetic Programming
- Standard Genetic Programming
- Random Constant
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Lyne, P.D.: Structure-based virtual screening: an overview. Drug Discovery Today 7, 1047–1055 (2002)
Kramer, B., Rarey, M., Lengauer, T.: Evaluation of the flexx incremental construction algorithm for protein-ligand docking. PROTEINS 37, 228–241 (1999)
Jones, G., Willett, P., Glen, R., Leach, A., Taylor, R.: Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267, 727–748 (1997)
Nissink, J., Murray, C., Hartshorn, M., Verdonk, M., Cole, J., Taylor, R.: A new test set for validating predictions of protein-ligand interaction. PROTEINS 49, 457–471 (2002)
Stahl, M., Böhm, H.J.: Development of filter functions for protein-ligand docking. J. Mol. Graphics Mod. 16, 121–132 (1998)
Smith, R., Hubbard, R., Gschwend, D., Leach, A., Good, A.: Analysis and optimization of structure-based virtual screening protocols (3). new methods and old problems in scoring function design. J. Mol. Graphics Mod. 22, 41–53 (2003)
Morley, S., Juhos, S., Garmendia-Doval, A.: rDock: a fast and accurate docking software for virtual screening (2003) (in preparation)
Afshar, M., Morley, S.: Validation of an empirical rna-ligand scoring function for fast flexible docking using ribodock (2003) (in preparation)
Crammer, N.L.: A representation for the adaptive generation of simple sequential programs. In: Grefenstette, J.J. (ed.) Proceedings of an International Conference on Genetic Algorithms and their Applications, pp. 183–187 (1985)
Koza, J.R.: Genetic Programming: On the Programming of Computers by Means of Natural Selection. MIT Press, Cambridge (1992)
Miller, J.F., Thomson, P.: Cartesian genetic programming. In: Poli, R., Banzhaf, W., Langdon, W.B., Miller, J., Nordin, P., Fogarty, T.C. (eds.) EuroGP 2000. LNCS, vol. 1802, pp. 121–132. Springer, Heidelberg (2000)
Miller, J.F.: What is a good genotype-phenotype mapping for the evolution of computer programs? Technical Report 364, University of Hertfordshire, Computer Science, University of Hertfordshire (2002)
Altenberg, L.: Emergent phenomena in genetic programming. In: Sebald, A.V., Fogel, L.J. (eds.) Evolutionary Programming — Proceedings of the Third Annual Conference, pp. 233–241. World Scientific Publishing, Singapore (1994)
Miller, J.: What bloat? cartesian genetic programming on boolean problems. In: Goodman, E.D. (ed.) 2001 Genetic and Evolutionary Computation Conference Late Breaking Papers, San Francisco, California, USA, pp. 295–302 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Garmendia-Doval, A.B., Morley, S.D., Juhos, S. (2004). Post Docking Filtering Using Cartesian Genetic Programming. In: Liardet, P., Collet, P., Fonlupt, C., Lutton, E., Schoenauer, M. (eds) Artificial Evolution. EA 2003. Lecture Notes in Computer Science, vol 2936. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24621-3_16
Download citation
DOI: https://doi.org/10.1007/978-3-540-24621-3_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-21523-3
Online ISBN: 978-3-540-24621-3
eBook Packages: Springer Book Archive